Module: HDF5::DataHelpers

Defined in:
lib/hdf5/data_helpers.rb

Class Method Summary collapse

Class Method Details

.array_shape(value) ⇒ Object 



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# File 'lib/hdf5/data_helpers.rb', line 84

def array_shape(value)
  return [] unless value.is_a?(Array)
  return [0] if value.empty?

  unless value.first.is_a?(Array)
    raise ShapeError, 'Data must be rectangular' if value.any? { |item| item.is_a?(Array) }

    return [value.length]
  end

  child_shape = array_shape(value.first)
  index = 1
  while index < value.length
    item = value[index]
    unless item.is_a?(Array) && array_shape(item) == child_shape
      raise ShapeError, 'Data must be rectangular'
    end
    index += 1
  end

  [value.length, *child_shape]
end

.buffer_for(narray) ⇒ Object

Raises:



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# File 'lib/hdf5/data_helpers.rb', line 162

def buffer_for(narray)
  dtype = DType.for_numo(narray)
  binary = if dtype.kind == :bool
             narray.to_a.flatten.map { |value| value.zero? ? 0 : 1 }.pack('C*')
           else
             narray.to_binary
           end
  expected_bytes = narray.size * dtype.itemsize
  raise HDF5::Error, 'Numo binary representation has an unexpected size' unless binary.bytesize == expected_bytes

  ::FFI::MemoryPointer.new(:char, expected_bytes).tap { |buffer| buffer.put_bytes(0, binary) }
end

.from_binary(dtype, binary, shape) ⇒ Object 



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# File 'lib/hdf5/data_helpers.rb', line 175

def from_binary(dtype, binary, shape)
  return dtype.numo_class.from_binary(binary, shape) unless dtype.kind == :bool

  bytes = binary.unpack('C*')
  return Numo::Bit.new.store(bytes.first) if shape.empty?

  Numo::UInt8.cast(bytes).reshape(*shape).ne(0)
end

.inferred_dtype(values, label:) ⇒ Object 



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# File 'lib/hdf5/data_helpers.rb', line 58

def inferred_dtype(values, label:)
  kind = nil
  minimum = maximum = 0
  values.each do |value|
    if value.is_a?(Integer)
      current = :int64
      minimum = value if value < minimum
      maximum = value if value > maximum
    elsif value.is_a?(Complex)
      current = :complex128
    elsif value.is_a?(Numeric)
      current = :float64
    elsif value.equal?(true) || value.equal?(false)
      current = :bool
    else
      raise HDF5::Error, "Only numeric #{label.downcase} is supported"
    end
    if kind && (kind == :bool) != (current == :bool)
      raise HDF5::Error, "Only numeric #{label.downcase} is supported"
    end
    kind = current if kind.nil? || current == :complex128 || current == :float64 && kind == :int64
  end
  kind = :uint64 if kind == :int64 && minimum >= 0 && maximum >= (1 << 63)
  DType.for_symbol(kind)
end

.normalize_booleans(value) ⇒ Object 



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# File 'lib/hdf5/data_helpers.rb', line 184

def normalize_booleans(value)
  return value.map { |item| normalize_booleans(item) } if value.is_a?(Array)

  value ? 1 : 0
end

.normalize_data(data, label: 'Data', dtype: nil, casting: :safe, convert: true) ⇒ Object

Raises:

  • (ArgumentError) 


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# File 'lib/hdf5/data_helpers.rb', line 5

def normalize_data(data, label: 'Data', dtype: nil, casting: :safe, convert: true)
  raise ArgumentError, "Unsupported casting mode: #{casting.inspect}" unless i[safe unsafe].include?(casting)

  if data.is_a?(Numo::NArray)
    source = DType.for_numo(data)
    return data unless dtype
    unless source.castable_to?(dtype, casting:)
      raise ConversionError, "Cannot safely cast #{source.to_sym} to #{dtype.to_sym}"
    end
    return data if source.to_sym == dtype.to_sym
    # HDF5 converts numeric widths and matching complex compounds directly,
    # but cannot convert a real numeric datatype to a complex compound.
    native_conversion = dtype.kind != :complex || source.kind == :complex
    return data if !convert && casting == :safe && native_conversion

    return dtype.numo_class.cast(data)
  end

  # Homogeneous flat Arrays need no recursive shape traversal or per-value
  # conversion checks: integer extrema cover the range; Ruby Float is float64.
  if dtype.nil? && data.is_a?(Array) && !data.empty?
    homogeneous = normalize_homogeneous_array(data, data, casting:)
    return homogeneous if homogeneous
  end

  shape = array_shape(data)
  values = data.is_a?(Array) ? (shape.length <= 1 ? data : data.flatten) : [data]
  raise HDF5::Error, "#{label} must not be empty without an explicit dtype" if values.empty? && !dtype
  if dtype.nil? && shape.length > 1
    homogeneous = normalize_homogeneous_array(data, values, casting:)
    return homogeneous if homogeneous
  end

  dtype ||= inferred_dtype(values, label:)
  validate_values(values, dtype, casting:)
  normalized = dtype.kind == :bool ? normalize_booleans(data) : data
  return dtype.numo_class.new(*shape) if values.empty?
  return Numo::Bit.new.store(normalized) if dtype.kind == :bool && !data.is_a?(Array)

  dtype.numo_class.cast(normalized)
end

.normalize_homogeneous_array(data, values, casting:) ⇒ Object 



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# File 'lib/hdf5/data_helpers.rb', line 47

def normalize_homogeneous_array(data, values, casting:)
  if values.all? { |value| value.is_a?(Integer) }
    minimum, maximum = values.minmax
    dtype = DType.for_symbol(minimum >= 0 && maximum >= (1 << 63) ? :uint64 : :int64)
    validate_values([minimum, maximum], dtype, casting:)
    dtype.numo_class.cast(data)
  elsif values.all? { |value| value.is_a?(Float) }
    Numo::DFloat.cast(data)
  end
end

.scalar?(value) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hdf5/data_helpers.rb', line 107

def scalar?(value)
  value.is_a?(Numeric) || value.equal?(true) || value.equal?(false) ||
    value.is_a?(Numo::NArray) && value.shape.empty?
end

.validate_component(component, size, dtype) ⇒ Object

Raises:



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# File 'lib/hdf5/data_helpers.rb', line 148

def validate_component(component, size, dtype)
  return if size == 8 && component.is_a?(Float)

  raise ConversionError, "Cannot safely cast complex data to #{dtype.to_sym}" if component.is_a?(Complex)

  converted = component.to_f
  converted = [converted].pack('f').unpack1('f') if size == 4
  return if component.is_a?(Float) && !component.finite? && !converted.finite?
  return if component.is_a?(Float) && component == converted
  return if converted.finite? && converted.to_r == component.to_r

  raise ConversionError, "Value #{component.inspect} cannot safely be represented as #{dtype.to_sym}"
end

.validate_values(values, dtype, casting:) ⇒ Object 



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# File 'lib/hdf5/data_helpers.rb', line 112

def validate_values(values, dtype, casting:)
  if dtype.kind == :bool
    unless values.all? { |value| value.equal?(true) || value.equal?(false) }
      raise ConversionError, 'Bool data must contain true or false'
    end
    return
  end
  if casting == :unsafe
    raise ConversionError, 'Data must contain numeric values' unless values.all? { |value| value.is_a?(Numeric) }
    return
  end

  case dtype.kind
  when :integer
    bits = dtype.itemsize * 8
    minimum = dtype.unsigned? ? 0 : -(1 << (bits - 1))
    maximum = dtype.unsigned? ? (1 << bits) - 1 : (1 << (bits - 1)) - 1
    values.each do |value|
      unless value.is_a?(Integer) && value.between?(minimum, maximum)
        raise ConversionError, "Value #{value.inspect} cannot safely be represented as #{dtype.to_sym}"
      end
    end
  when :float, :complex
    size = dtype.kind == :complex ? dtype.itemsize / 2 : dtype.itemsize
    values.each do |value|
      raise ConversionError, 'Data must contain numeric values' unless value.is_a?(Numeric)
      if dtype.kind == :complex
        validate_component(value.real, size, dtype)
        validate_component(value.imag, size, dtype)
      else
        validate_component(value, size, dtype)
      end
    end
  end
end